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Calcium in PDB 2d2o: Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft

Enzymatic activity of Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft

All present enzymatic activity of Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft:
3.2.1.135;

Protein crystallography data

The structure of Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft, PDB code: 2d2o was solved by A.Ohtaki, M.Mizuno, H.Yoshida, T.Tonozuka, Y.Sakano, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.690, 118.710, 112.380, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft (pdb code 2d2o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft, PDB code: 2d2o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2d2o

Go back to Calcium Binding Sites List in 2d2o
Calcium binding site 1 out of 2 in the Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:24.1
occ:1.00
 OD2 A:ASP149 2.2 26.4 1.0
O A:HOH1215 2.3 22.6 1.0
OD2 A:ASP171 2.3 22.7 1.0
O A:ASP145 2.4 20.3 1.0
OD1 A:ASN148 2.4 22.3 1.0
O A:GLY169 2.5 20.8 1.0
OD1 A:ASN143 2.5 21.6 1.0
CG A:ASN143 3.2 22.8 1.0
C A:ASP145 3.3 21.0 1.0
CG A:ASP171 3.4 25.0 1.0
CG A:ASP149 3.5 27.2 1.0
C A:GLY169 3.5 21.8 1.0
CG A:ASN148 3.6 25.1 1.0
ND2 A:ASN143 3.7 19.0 1.0
CB A:ASP171 3.9 23.3 1.0
CA A:GLY169 4.0 19.8 1.0
N A:ASP149 4.0 26.8 1.0
ND2 A:ASN148 4.1 24.2 1.0
N A:PRO146 4.1 22.4 1.0
N A:ASP145 4.1 21.3 1.0
CA A:PRO146 4.2 23.4 1.0
CA A:ASP145 4.2 20.5 1.0
OD1 A:ASP149 4.2 28.0 1.0
CA A:ASP149 4.2 27.9 1.0
O A:GLN215 4.3 23.4 1.0
CB A:ASN143 4.4 22.4 1.0
C A:ASN148 4.4 26.0 1.0
CB A:ASP149 4.5 26.8 1.0
CA A:ASN143 4.5 22.9 1.0
OD1 A:ASP171 4.5 21.4 1.0
CB A:ASP145 4.5 21.1 1.0
C A:GLY170 4.6 20.4 1.0
C A:PRO146 4.7 21.8 1.0
O A:GLY170 4.7 21.4 1.0
N A:ASN148 4.7 23.9 1.0
N A:GLY170 4.7 20.6 1.0
N A:ASP171 4.7 21.5 1.0
CB A:ASN148 4.8 24.7 1.0
C A:ASN143 4.8 22.6 1.0
O A:ASN148 4.8 25.3 1.0
CA A:ASN148 4.9 24.6 1.0
N A:GLY144 4.9 21.9 1.0
CA A:ASP171 5.0 22.2 1.0
O A:PRO146 5.0 20.6 1.0

Calcium binding site 2 out of 2 in 2d2o

Go back to Calcium Binding Sites List in 2d2o
Calcium binding site 2 out of 2 in the Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:32.4
occ:1.00
 OD1 B:ASP149 2.2 35.0 1.0
OD1 B:ASN148 2.4 28.3 1.0
OD1 B:ASP171 2.4 25.5 1.0
O B:GLY169 2.4 27.4 1.0
O B:HOH1077 2.5 36.7 1.0
O B:ASP145 2.5 35.5 1.0
OD1 B:ASN143 2.5 30.4 1.0
CG B:ASN143 3.3 31.4 1.0
C B:ASP145 3.3 35.5 1.0
CG B:ASP149 3.4 34.8 1.0
CG B:ASN148 3.4 29.9 1.0
CG B:ASP171 3.5 29.1 1.0
C B:GLY169 3.5 29.0 1.0
ND2 B:ASN143 3.7 32.4 1.0
CB B:ASP171 3.9 28.1 1.0
N B:ASP149 3.9 34.2 1.0
ND2 B:ASN148 3.9 32.2 1.0
CA B:GLY169 3.9 28.2 1.0
N B:PRO146 4.0 37.3 1.0
CA B:PRO146 4.0 37.4 1.0
N B:ASP145 4.1 33.4 1.0
CA B:ASP149 4.1 35.3 1.0
OD2 B:ASP149 4.2 35.0 1.0
CA B:ASP145 4.2 34.5 1.0
O B:GLN215 4.3 30.1 1.0
CB B:ASN143 4.4 30.3 1.0
C B:ASN148 4.4 34.2 1.0
CB B:ASP149 4.4 34.3 1.0
CA B:ASN143 4.4 31.3 1.0
OD2 B:ASP171 4.5 28.9 1.0
C B:GLY170 4.6 26.7 1.0
O B:GLY170 4.6 27.3 1.0
C B:PRO146 4.6 36.8 1.0
N B:GLY170 4.6 29.2 1.0
N B:ASN148 4.7 34.5 1.0
CB B:ASP145 4.7 34.7 1.0
CB B:ASN148 4.7 32.8 1.0
N B:ASP171 4.8 27.1 1.0
C B:ASN143 4.8 31.5 1.0
CA B:ASN148 4.8 33.6 1.0
N B:GLY144 4.8 31.0 1.0
O B:ASN148 4.9 35.3 1.0
O B:HOH1248 5.0 32.2 1.0
CA B:ASP171 5.0 26.7 1.0
CA B:GLY170 5.0 25.9 1.0

Reference:

A.Ohtaki, M.Mizuno, H.Yoshida, T.Tonozuka, Y.Sakano, S.Kamitori. Structure of A Complex of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 with Maltohexaose Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding Cleft Carbohydr.Res. V. 341 1041 2006.
ISSN: ISSN 0008-6215
PubMed: 16564038
DOI: 10.1016/J.CARRES.2006.01.029
Page generated: Sat Dec 12 03:34:42 2020

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